BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 003028
(856 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 37/172 (21%), Positives = 72/172 (41%), Gaps = 9/172 (5%)
Query: 381 KLLDQMVRDGCQPNVVTYNRLIHSYGRANYLNEA---------LDVFKQMQVVGCEPDRV 431
+L D+ R+G Q + YN L++ A E+ D+FKQM V P+
Sbjct: 47 RLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEA 106
Query: 432 TYCTLIDIHAKAGFLDVAMDMYKKMQAAGLSPDTFTYSVIINCLGKAGHLQAAHQLFCEM 491
T+ + ++A DM K+M+A G+ P +Y + + G A+++ M
Sbjct: 107 TFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM 166
Query: 492 VNQGCIPNLVTYNIMIALQAKARNYQSALKLYRDMQNAGFEPDKVTYSIVME 543
V +P ++ + +N K + +++ + K T+ ++ E
Sbjct: 167 VESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEE 218
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 30/136 (22%), Positives = 58/136 (42%), Gaps = 13/136 (9%)
Query: 437 IDIHAKAGFLDVAMDMYKKMQAAGLSPDTFTYSVI--INCLGKAGH-------LQAAHQL 487
+D+ +K G + A+ +Y + + G+ + Y+V+ + L +A L +
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 488 FCEMVNQGCIPNLVTYNIMIALQAKARNYQSALKLYRDMQNAGFEPDKVTYSIVMEVLGH 547
F +M+ +PN T+ L + + A + + M+ G +P +Y + G
Sbjct: 93 FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPAL--FGF 150
Query: 548 C--GYLDEAEAVFAEM 561
C G D+A V A M
Sbjct: 151 CRKGDADKAYEVDAHM 166
>pdb|2WZF|A Chain A, Legionella Pneumophila Glucosyltransferase Crystal
Structure
Length = 525
Score = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 46/110 (41%), Gaps = 21/110 (19%)
Query: 406 GRANYLNEALDVFKQ----MQVVGCEPDRVTYCTLIDIHAKAGFLDVAMDMYKKMQAAGL 461
++ Y+NE + F + + ++ +P ++ TL + AKA ++D+A + Y L
Sbjct: 385 AQSKYINEHISEFSEKDLLLNLISDKPSEISQHTLDFVKAKAMYIDIAKEHYSAFYKP-L 443
Query: 462 SPDTFTYSVIINCLGKAGHLQAAH----------------QLFCEMVNQG 495
+ I N LG AG H Q+FC+ ++G
Sbjct: 444 VEEISGPGAIYNALGGAGSFTTTHRRLTGPMLPTTPPRVLQVFCDAHDKG 493
>pdb|2VGL|B Chain B, Ap2 Clathrin Adaptor Core
pdb|2JKR|B Chain B, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|E Chain E, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|B Chain B, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|E Chain E, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
Length = 591
Score = 33.1 bits (74), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 689 NVRDHVGSFLEMMHSEDRESKRGLVDAVVD-FLHK-SGLKEEAGSVWEVAAQKNVYPDAV 746
N + + SFLE H E + + L+ A+V FL K S +E V +A Q + PD +
Sbjct: 461 NADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPD-L 519
Query: 747 KEKGMSYW 754
+++G YW
Sbjct: 520 RDRGYIYW 527
>pdb|2XA7|B Chain B, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 592
Score = 33.1 bits (74), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 689 NVRDHVGSFLEMMHSEDRESKRGLVDAVVD-FLHK-SGLKEEAGSVWEVAAQKNVYPDAV 746
N + + SFLE H E + + L+ A+V FL K S +E V +A Q + PD +
Sbjct: 461 NADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPD-L 519
Query: 747 KEKGMSYW 754
+++G YW
Sbjct: 520 RDRGYIYW 527
>pdb|3NCY|W Chain W, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
pdb|3NCY|S Chain S, X-Ray Crystal Structure Of An Arginine Agmatine Antiporter
(Adic) In Complex With A Fab Fragment
Length = 211
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 97 VDAVPKDVLTSSPISDQFVKAGVAAVCFLSDL----VNYKLPALDGSGTANSPTNFMVD 151
DA P V P S+Q G + VCFL++ +N K +DGS N N D
Sbjct: 108 ADAAPT-VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKKIDGSERQNGVLNSWTD 165
>pdb|1QNW|A Chain A, Lectin Ii From Ulex Europaeus
pdb|1QNW|B Chain B, Lectin Ii From Ulex Europaeus
pdb|1QNW|C Chain C, Lectin Ii From Ulex Europaeus
pdb|1QNW|D Chain D, Lectin Ii From Ulex Europaeus
pdb|1QOO|A Chain A, Lectin Uea-Ii Complexed With Nag
pdb|1QOO|B Chain B, Lectin Uea-Ii Complexed With Nag
pdb|1QOO|C Chain C, Lectin Uea-Ii Complexed With Nag
pdb|1QOO|D Chain D, Lectin Uea-Ii Complexed With Nag
pdb|1QOT|A Chain A, Lectin Uea-Ii Complexed With Fucosyllactose And
Fucosylgalactose
pdb|1QOT|B Chain B, Lectin Uea-Ii Complexed With Fucosyllactose And
Fucosylgalactose
pdb|1QOT|C Chain C, Lectin Uea-Ii Complexed With Fucosyllactose And
Fucosylgalactose
pdb|1QOT|D Chain D, Lectin Uea-Ii Complexed With Fucosyllactose And
Fucosylgalactose
pdb|1QOS|A Chain A, Lectin Uea-Ii Complexed With Chitobiose
pdb|1QOS|B Chain B, Lectin Uea-Ii Complexed With Chitobiose
pdb|1DZQ|A Chain A, Lectin Uea-Ii Complexed With Galactose
pdb|1DZQ|B Chain B, Lectin Uea-Ii Complexed With Galactose
pdb|1DZQ|C Chain C, Lectin Uea-Ii Complexed With Galactose
pdb|1DZQ|D Chain D, Lectin Uea-Ii Complexed With Galactose
Length = 242
Score = 30.0 bits (66), Expect = 5.2, Method: Composition-based stats.
Identities = 21/94 (22%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 52 YTPARAGVVVSGEAA-KAAGLQKSERVSVPSPSSLGRSDHVSYASSVDAVPKDVLTSSPI 110
+ P + ++ G+A+ G+ + +VS P+ +S+GR+ + + D++ V + +
Sbjct: 13 FVPNQKNIIFQGDASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSITGKVASFATS 72
Query: 111 SDQFVKA----GVAAVCFLSDLVNYKLPALDGSG 140
VKA GV + F N ++P+ +G
Sbjct: 73 FSFVVKADKSDGVDGLAFFLAPANSQIPSGSSAG 106
>pdb|2BS2|C Chain C, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|2BS2|F Chain F, Quinol:fumarate Reductase From Wolinella Succinogenes
Length = 256
Score = 30.0 bits (66), Expect = 5.5, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 571 PVYGLL---VDLWGKAGNVRKA--WEWYEAMLQAGLRPNVPTCNSLLSAFLRV-GQLSDA 624
P+Y +L V+L G G R A W W++ R N+ +L+SAFL V G L+
Sbjct: 170 PLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPDKTRANLKKLKTLMSAFLIVLGLLTFG 229
Query: 625 YHLLQGM 631
++ +G+
Sbjct: 230 AYVKKGL 236
>pdb|1E7P|C Chain C, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|F Chain F, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|I Chain I, Quinol:fumarate Reductase From Wolinella Succinogenes
pdb|1E7P|L Chain L, Quinol:fumarate Reductase From Wolinella Succinogenes
Length = 256
Score = 30.0 bits (66), Expect = 5.5, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 571 PVYGLL---VDLWGKAGNVRKA--WEWYEAMLQAGLRPNVPTCNSLLSAFLRV-GQLSDA 624
P+Y +L V+L G G R A W W++ R N+ +L+SAFL V G L+
Sbjct: 170 PLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPDKTRANLKKLKTLMSAFLIVLGLLTFG 229
Query: 625 YHLLQGM 631
++ +G+
Sbjct: 230 AYVKKGL 236
>pdb|1QLB|C Chain C, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
pdb|1QLB|F Chain F, Respiratory Complex Ii-Like Fumarate Reductase From
Wolinella Succinogenes
Length = 256
Score = 30.0 bits (66), Expect = 5.5, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 571 PVYGLL---VDLWGKAGNVRKA--WEWYEAMLQAGLRPNVPTCNSLLSAFLRV-GQLSDA 624
P+Y +L V+L G G R A W W++ R N+ +L+SAFL V G L+
Sbjct: 170 PLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPDKTRANLKKLKTLMSAFLIVLGLLTFG 229
Query: 625 YHLLQGM 631
++ +G+
Sbjct: 230 AYVKKGL 236
>pdb|2HMI|C Chain C, Hiv-1 Reverse TranscriptaseFRAGMENT OF FAB 28DNA COMPLEX
pdb|1J5O|L Chain L, Crystal Structure Of Met184ile Mutant Of Hiv-1 Reverse
Transcriptase In Complex With Double Stranded Dna
Template- Primer
Length = 214
Score = 30.0 bits (66), Expect = 5.7, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 98 DAVPKDVLTSSPISDQFVKAGVAAVCFLSDLVNYKLP---ALDGSGTANSPTNFMVD 151
DA P V P S+Q G + VCFL++ + A+DGS AN N D
Sbjct: 110 DAAPT-VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVAWAIDGSAAANGVLNSWTD 165
>pdb|1HYS|C Chain C, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With A Polypurine Tract Rna:dna
Length = 214
Score = 30.0 bits (66), Expect = 5.9, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 98 DAVPKDVLTSSPISDQFVKAGVAAVCFLSDLVNYKLP---ALDGSGTANSPTNFMVD 151
DA P V P S+Q G + VCFL++ + A+DGS AN N D
Sbjct: 110 DAAPT-VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVAWAIDGSAAANGVLNSWTD 165
>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha.
pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha
Length = 388
Score = 29.6 bits (65), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 36/159 (22%), Positives = 67/159 (42%), Gaps = 13/159 (8%)
Query: 431 VTYCTLIDIHAKAGFLDVAMDMYKK-MQAAGLSPDTFTYSVIINCLGKAGHLQAAHQLFC 489
V + L ++ + G +D+A+D Y++ ++ PD Y + N L + G + A +
Sbjct: 238 VVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPD--AYCNLANALKEKGSVAEAEDCYN 295
Query: 490 EMVNQGCIPNLVTYNIMIALQAKARNYQSALKLYRDMQNAGFEPDKVTYSIVMEVLGHCG 549
+ + C + + N + ++ + N + A++LYR F +S + VL G
Sbjct: 296 TAL-RLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEV-FPEFAAAHSNLASVLQQQG 353
Query: 550 YLDEAEAVFAEMRRKNWVPDEPVYGLLVDLWGKAGNVRK 588
L E A M K + P + D + GN K
Sbjct: 354 KLQE-----ALMHYKEAIRISPTFA---DAYSNMGNTLK 384
>pdb|1VRM|A Chain A, Crystal Structure Of The Apbe Protein (Tm1553) From
Thermotoga Maritima Msb8 At 1.58 A Resolution
Length = 325
Score = 29.3 bits (64), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 14/69 (20%)
Query: 517 QSALKLYRDMQNAGFEPDKVTYSIVMEVLGHCGYLDEAEAVFAEMRRKNWVPDEPVYGLL 576
+S +K D N E D+ TYS++ +A FAE+ + +P G L
Sbjct: 65 RSVVKKINDHPNEWVEVDEETYSLI-----------KAACAFAELTDGAF---DPTVGRL 110
Query: 577 VDLWGKAGN 585
++LWG GN
Sbjct: 111 LELWGFTGN 119
>pdb|3OKK|A Chain A, Crystal Structure Of S25-39 In Complex With Kdo(2.4)kdo
Length = 220
Score = 29.3 bits (64), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 97 VDAVPKDVLTSSPISDQFVKAGVAAVCFLSDL----VNYKLPALDGSGTANSPTNFMVD 151
DA P V P S+Q G + VCFL++ +N K +DGS AN N D
Sbjct: 114 ADAAPT-VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKW-KIDGSERANGVLNSWTD 170
>pdb|3OKD|A Chain A, Crystal Structure Of S25-39 In Complex With Kdo
pdb|3OKE|A Chain A, Crystal Structure Of S25-39 In Complex With Ko
pdb|3OKL|A Chain A, Crystal Structure Of S25-39 In Complex With Kdo(2.8)kdo
pdb|3OKM|A Chain A, Crystal Structure Of Unliganded S25-39
pdb|3OKN|A Chain A, Crystal Structure Of S25-39 In Complex With
Kdo(2.4)kdo(2.4)kdo
pdb|3OKO|A Chain A, Crystal Structure Of S25-39 In Complex With
Kdo(2.8)kdo(2.4)kdo
Length = 219
Score = 29.3 bits (64), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 97 VDAVPKDVLTSSPISDQFVKAGVAAVCFLSDL----VNYKLPALDGSGTANSPTNFMVD 151
DA P V P S+Q G + VCFL++ +N K +DGS AN N D
Sbjct: 114 ADAAPT-VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKW-KIDGSERANGVLNSWTD 170
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.132 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,180,956
Number of Sequences: 62578
Number of extensions: 1038404
Number of successful extensions: 2741
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 2736
Number of HSP's gapped (non-prelim): 46
length of query: 856
length of database: 14,973,337
effective HSP length: 107
effective length of query: 749
effective length of database: 8,277,491
effective search space: 6199840759
effective search space used: 6199840759
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)